Proteins play a pivotal role in virtually every cellular function. They are responsible for molecular transport, provide structural support, and participate in defence mechanisms. Proteins, known as enzymes, act as catalysts, speeding up biochemical reactions. Other proteins are responsible for intercellular communications.
Functions of proteins
Image source: Biorender.com
Proteins are made of amino acids
A polymer formed by the linkage of amino acids is termed a polypeptide and is called a protein when it serves a biological function. Any compound containing both an amino group (-NH2) and a carboxylic group (-COOH) can be broadly termed an amino acid. Yet, it is specifically the α-amino acids, where the amino and carboxylic groups are attached to the same carbon atom, that are the building blocks of proteins. The side chain, which can as well be called the R group, is variable among amino acids.
Amino acid structure
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OpenStax College - Anatomy & Physiology, Connexions Web site. http://cnx.org/content/col11496/1.6/, Jun 19, 2013., CC BY 3.0, https://commons.wikimedia.org/w/index.php?curid=30131160
A total of 22 amino acids can be incorporated into polypeptides by ribosomes. Notably, among these, 20 amino acids are considered "canonical" and are universally present in all organisms. The distinctive properties of a particular amino acid are defined by its side chain, which can be categorised as negatively charged (acidic), positively charged (basic), nonpolar (hydrophobic), or polar (hydrophilic).
Proteinogenic amino acids
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CNX OpenStax - http://cnx.org/contents/[email protected]:rZudN6XP@2/Introduction, CC BY 4.0, https://commons.wikimedia.org/w/index.php?curid=49923700
A linkage between a carboxyl group of one amino acid and an amino group of another amino acid is called a peptide bond.
Formation of a peptide bond by a dehydration reaction
Levels of protein structure
Following synthesis by a ribosome, a polypeptide undergoes a folding process, dictated by the sequence of amino acids. The resulting complex shape of the protein and the physical properties of its surface govern its capability to interact with other molecules and determine its function. The structure of proteins can be classified into four levels: primary, secondary, tertiary, and, in some cases, quaternary.
Levels of protein structure
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CNX OpenStax - https://cnx.org/contents/[email protected], CC BY 4.0, https://commons.wikimedia.org/w/index.php?curid=53712842
The primary structure is the sequence of amino acids in a peptide. The primary structure of a protein is defined by the genetic information encoded in the DNA.
The secondary structure is a regular local conformation of the polypeptide backbone stabilised by hydrogen bonds between carboxyl oxygen atoms and hydrogen atoms attached to nitrogen atoms. Two common types of secondary structures include the spiral-shaped alpha helix and the beta-pleated sheet, the latter formed by two or several parallel polypeptide segments.
Secondary structures: alpha helix and beta-pleated sheet
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CNX OpenStax - https://cnx.org/contents/[email protected], CC BY 4.0, https://commons.wikimedia.org/w/index.php?curid=53712849
The tertiary structure refers to the overall three-dimensional shape of a polypeptide and is stabilised by interactions between amino acids' R groups. These interactions include hydrogen bonds, ionic bonds, disulfide bridges formed between cysteine residues, van der Waals forces, and hydrophobic interactions. The latter entails the grouping of hydrophobic amino acid residues at the core of a protein globule to minimise contact with water, while hydrophilic amino acid residues predominantly occupy the surface, exposed to the aqueous environment.
Interactions stabilising the tertiary structure
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CNX OpenStax - https://cnx.org/contents/[email protected], CC BY 4.0, https://commons.wikimedia.org/w/index.php?curid=53712850
The quaternary structure represents the overall structure of a protein, formed by the arrangement of two or several polypeptides referred to as subunits. A classic example is haemoglobin consisting of two α globin and two β globin subunits, each carrying a non-protein haem group.
Haemoglobin structure. α globin and β globin subunits are shown in red and blue respectively. Haem groups are shown in green.
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Zephyris at the English-language Wikipedia, CC BY-SA 3.0, https://commons.wikimedia.org/w/index.php?curid=2300973
Overall, the diversity of functions performed by proteins is reflected by the diversity of their shapes.
Examples of proteins' 3D shapes
Image source:
David Goodsell, https://book.bionumbers.org/how-big-is-the-average-protein/, with changes
